6FRA
F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6EH6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | 30% PEG 8K, 0.1M MES, 0.2M Na Acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 51.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.71 | α = 90 |
b = 114.63 | β = 90 |
c = 50.66 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2012-10-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9200 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||
1 | 1.73 | 47.64 | 99.9 | 0.06 | 0.065 | 0.999 | 19.2 | 6.6 | 52808 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.73 | 1.78 | 100 | 0.783 | 0.847 | 6.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6EH6 | 1.73 | 47.64 | 50066 | 2690 | 99.88 | 0.20545 | 0.2034 | 0.24339 | RANDOM | 29.76 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.52 | 1.6 | -2.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.452 |
r_dihedral_angle_4_deg | 17.387 |
r_dihedral_angle_3_deg | 16.399 |
r_dihedral_angle_1_deg | 7.914 |
r_angle_refined_deg | 2.038 |
r_angle_other_deg | 0.955 |
r_chiral_restr | 0.136 |
r_bond_refined_d | 0.019 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3487 |
Nucleic Acid Atoms | |
Solvent Atoms | 132 |
Heterogen Atoms | 65 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
UCSD-system | data reduction |
Aimless | data scaling |
PHASER | phasing |